Molecular and Genetic Characterization of MHC Deficiency Identifies EZH2 as Therapeutic Target for Enhancing Immune Recognition

Abstract

We performed a genomic, transcriptomic, and immunophenotypic study of 347 patients with diffuse large B-cell lymphoma (DLBCL) to uncover the molecular basis underlying acquired defi ciency of MHC expression. Low MHC-II expression defi nes tumors originating from the centroblast-rich dark zone of the germinal center (GC) that was associated with inferior prognosis. MHC-II-defi cient tumors were characterized by somatically acquired gene mutations reducing MHC-II expression and a lower amount of tumor-infi ltrating lymphocytes. In particular, we demonstrated a strong enrichment of EZH2 mutations in both MHC-I-and MHC-II-negative primary lymphomas, and observed reduced MHC expression and T-cell infi ltrates in murine lymphoma models expressing mutant Ezh2 Y641. Of clinical relevance, EZH2 inhibitors signifi cantly restored MHC expression in EZH2-mutated human DLBCL cell lines. Hence, our fi ndings suggest a tumor progression model of acquired immune escape in GC-derived lymphomas and pave the way for development of complementary therapeutic approaches combining immunotherapy with epigenetic reprogramming. SIGNIFICANCE: We demonstrate how MHC-defi cient lymphoid tumors evolve in a cell-of-origin-specifi c context. Specifi cally, EZH2 mutations were identifi ed as a genetic mechanism underlying acquired MHC defi ciency. The paradigmatic restoration of MHC expression by EZH2 inhibitors provides the rationale for synergistic therapies combining immunotherapies with epigenetic reprogramming to enhance tumor recognition and elimination.

Germinal center‐derived lymphomas: The darkest side of humoral immunity

“…Lymphomas arise from failure of GC exit signals to restore expression of these genes through several proposed epigenetic mechanisms: (A) EZH2 is induced in GC B cells and converts H3K4me3 active promoters (green) to H3K4me3/H3K27me3 bivalent promoters (yellow) for transient repression of target genes, which is reversed upon GC exit. 16,17,21,114 It is not yet known how the EZH2 H3K27 methylation program is erased in the light zone, but it is reasonable to postulate that this is essential for GC exit. 16,112,113 Conditional deletion of EZH2 in GC B cells results in failure to form GCs.…”

“…58 Mutations in this pathway may enable GC B cells, which are normally largely confined to their respective follicles, to spread to other sites resulting in systemic dissemination. 114 This repression is due at least in part to increased levels of the H3K27me3 repressive mark at antigen presentation genes, an effect that can be overcome by EZH2 inhibitors. 165 Somatic mutation of EZH2 is associated with profound silencing of both MHC I and MHC II genes, and EZH2-mutant lymphomas in both mouse and humans manifest reduced expression of these genes and a reduction in lymphoma infiltrating CD4 and CD8 T cells.…”

“…MHC class II-dependent manner. 114 Finally, MHC class II expression may also be affected by the differentiation status of the cells, as seen in the more plasmablastic ABC-DLBCLs that also feature low MHC II levels. 114 This repression is due at least in part to increased levels of the H3K27me3 repressive mark at antigen presentation genes, an effect that can be overcome by EZH2 inhibitors.…”

“…16,187 Wildtype DLBCLs and FLs may also respond, given that EZH2 is an essential protein in GC B cells from which lymphomas arise. 114 Although current regimens involve continuous and prolonged dosing, this can lead to the development of resistance and may not be necessary if the drug is used in more brief cycles in combination. Among these, combination with BH3 mimetics was shown to be highly synergistic and is well suited to the setting of EZH2 mutant FLs and EZB DLBCLs.…”

“…21 Genes regulated in this manner include cell cycle checkpoint genes such as CDKN1A, antigen presentation genes, and GC exit genes such as IRF4. 16,17,21,114 It is not yet known how the EZH2 H3K27 methylation program is erased in the light zone, but it is reasonable to postulate that this is essential for GC exit. EZH2 is affected by somatic gainof-function mutations in 30% of GCB-DLBCL and FL patients.…”